Composition for a mitotic remodeling of chromosomes

ABSTRACT

A composition of a female germinal cell (egg) extract of pluricellular organisms in M-phase of the cell cycle, the extract being used for a mitotic remodeling of chromosomes of donor cells of pluricellular organisms, wherein the mitotic remodeling confers to the nucleus of the donor cells the ability to adapt themselves to the early embryonic development, in particular to the replication phases, in order to carry out the embryonic development or to obtain stem cells.

This application is a divisional of Ser. No. 12/088,697 filed Sep. 8,2008, now U.S. Pat. No. 8,753,887 which was filed pursuant to 35 USC 371as a United States National Phase Application of InternationalApplication No. PCT/EP2006/009499, filed Sep. 29, 2006 which claimspriority to U.S. Provisional Application 60/721,978, filed Sep. 30,2005.

SEQUENCE LISTING

An attached Substitute Sequence Listing (i. Name:SEQCRF_(—)0611-1003-2_ST25, ii. Date of Creation: Jun. 18, 2014, andiii. Size: 2 KB) is based on the Sequence Listing filed with U.S.application Ser. No. 14/269,431.

Nuclear transfer is a powerful method that can be used to produce clonedanimals and to obtain new sources of multipotential cells fromdifferentiated tissues. By transplanting nuclei from differentiatedamphibian or mammalian cells into enucleated eggs, blastula orblastocyst embryos can be obtained which can develop into entire animalsor used to form a wide range of tissues and cell types (Gurdon et al.,2003). The potential ability to deliver supplies of multipotentialcells, which hold great promise for cell-based therapies for numerousdisorders, makes nuclear transfer an appealing alternative to thedifficult practice of directly isolating natural stem cells from normaladult tissues (McKay, 2000).

Despite its many advantages, however, nuclear transplantation is ofteninefficient due to the difficulty involved in completely reprogrammingdifferentiated adult nuclei for the events of early development. Indeed,it is known that the ability of the egg to reset the epigenetic marks ofadult donor cells is determinant for the efficiency of nuclear cloning.Identifying the specific epigenetic properties of differentiated cellnuclei that must be reset before development can begin anew, and howsuch resetting can be efficiently achieved, thus represents a challengeof major biological and medical significance.

Various methods have been identified that can enhance the efficiency ofnuclear transplantation. In amphibians, for example, cloning efficiencyis substantially improved by serial nuclear transfers. This consists oftransferring a nucleus from a differentiated donor cell to an enucleatedegg, allowing the cell to undergo several divisions, and then using thedaughter nuclei as donors for a second nuclear transfer experiment(Gurdon, 1962). Injections of nuclei into maturing oocytes instead ofeggs (DiBerardino and Hoffner, 1983) led to the hypothesis thatcomponents of maturing oocytes may enable the injected nucleus torespond to DNA synthesis-inducing factors in activated eggs (Leonard etal., 1982).

One possible factor contributing to the low efficiency of cloningexperiments is that the chromosome organization of differentiated adultnuclei may not be well adapted for DNA replication. DNA replicationoccurs at several hundred foci within the nuclei of proliferating cells,with origins that appear to be synchronously set up prior to entry intoS phase (Jackson, 1990) These foci are stable throughout S phase, andcan persist across successive divisions (see (Berezney et al., 2000) forreview).

Animal cloning represents a major challenge in various fields, from theconservation of animal species, the production of proteins, such astherapeutic proteins, by cloned animals, to the therapeutic cloning,particularly for obtaining stems cells useful for autologoustransplants.

However, the efficiency of the current cloning techniques needs to beimproved to in order to contemplate large scale applications.

The present invention relates to the use of a cell extract for a mitoticremodeling of chromosomes and nuclei in order to adapt them to the celldivision characteristics of the early development and make them moresuitable for embryogenesis.

Another aspect of the invention is to provide a composition comprisingnuclei of donor cells or donor cells and a cell extract.

Another aim of the present invention is to provide a process for cloningcells of non-human pluricellular organisms.

Another aim of the invention is also to provide a process for obtainingmultipotent or totipotent stem cells of pluricellular organisms.

The present invention relates to the use of a female germinal cell (egg)extract of pluricellular organisms in M-phase of the cell cycle for amitotic remodeling of chromosomes of donor cells of pluricellularorganisms, wherein the mitotic remodeling confers to the nucleus of theaforesaid donor cells the ability to adapt themselves to the earlyembryonic development, in particular to the replication phases, in orderto carry out the embryonic development or to obtain stem cells.

The expression “germinal cell” refers to a cell susceptible to form thegametes.

The expression “female germinal cell”, also called “egg” relates a cellat any stage of the oogenesis, particularly primordial germ cells,oogonia and oocytes.

The germinal cell extract is preferentially made from eggs which arearrested at the metaphase stage of the second meiotic division.

The “female germinal cell (egg) extract” is a cell extract obtained bythe implementation of the process as described in Menut et al., 2001(referred as CSF extract).

In what precedes and what follows, the female germinal cell extract canbe replaced by a mitotic non-human early embryo of vertebrates. Saidmitotic non-human early embryo of vertebrates may be obtained by theprocess described in Lemaitre et al. 1998.

The expression “pluricellular organism” (or “multicellular organism”)refers to living organisms that are composed of several cells. In saidmulticellular or pluricellular organisms, the similar cells usuallyaggregate in tissues and the specific arrangements of different tissuesform organs.

The cell cycle is the cycle of life of a cell which undergoes division.The cell cycle comprises:

-   -   the M-phase, which corresponds to the mitosis wherein the        nucleus is divided, and    -   the interphase, which is constituted by the three following        phases:        -   G1-phase, which corresponds to the period of the interphase            that precedes the DNA synthesis,        -   S-phase, which corresponds to the phase of DNA synthesis,        -   G2-phase, which corresponds to the period of the interphase            that follows the DNA synthesis.

The “replication phase” corresponds to the phase of DNA synthesis, i.e.the S-phase of the cell cycle.

The expression “mitotic remodeling” refers to major changes in theorganization of the chromosomes or chromatin or the nucleus, which occurat mitosis.

By using the term “chromosome”, it is referred to the association of DNAand proteins that is present in the nucleus of all eukaryote cells, andwhich is particularly apparent during mitosis and meiosis.

The expression “early embryonic development” refers to the period fromfertilized ovum up to the occurrence of the first differentiated cells(not included).

In Xenopus, the early embryonic development corresponds to the periodfrom the fertilized egg up to a period encompassing the mid-blastulatransition and gastrulation and first transcriptions in the embryo.

The expression “adapt themselves to the early embryonic development”means that they can function as early embryonic nuclei.

One aim of the invention is to use the aforesaid female germinal cell(egg) extract for a mitotic remodeling of chromosomes of donor cells inorder to carry out the embryonic development. The expression “carry outthe embryonic development” means that the nucleus of the donor cell canbe introduced in an enucleated egg in order to perform its embryonicdevelopment.

Another aim of the invention is to use the aforesaid female germinalcell (egg) extract for a mitotic remodeling of chromosomes of donorcells in order to obtain stem cells.

Stem cells are primal undifferentiated cells that retain the ability todivide and can differentiate into other cell types. Totipotent stemcells can differentiate into embryonic and extra-embryonic cell types.Pluripotent stem cells originate from totipotent cells and can give riseto progeny that are derivatives of the three embryonic germ layers,mesoderm, ectoderm and endoderm.

The invention particularly relates to the use as defined above, whereinthe donor cells are differentiated somatic cells.

Somatic cells are any cells other than oocytes and spermatozoids.

“Differentiated somatic cells” are somatic cells that are specialized ina particular function and that do not maintain the ability to generateother kinds of cells or to revert back to a less differentiated state.

The differentiated somatic cells may particularly originate from anykind of tissue of the organism, such as skin, intestine, liver, blood,muscle, etc.

The invention also relates to the above mentioned use, wherein thefemale germinal cell (egg) extract of pluricellular organisms is inM-phase of the cell cycle and contains the material necessary to carryout the division cycles and the material necessary to allow the mitoticremodeling of the chromosomes.

In a preferred embodiment, the invention relates to the use as definedabove, wherein the pluricellular organisms are vertebrates chosen amongmammals, in particular humans, birds, reptiles and amphibians, andparticularly Xenopus.

In the context of the present invention, the mitotic extract and thedonor cell may originate from different species. In a preferredembodiment of the invention, the mitotic extract and the donor celloriginate from the same species.

The invention relates to a composition comprising nuclei of cells ofpluricellular organisms, preferentially permeabilized, and an extract ofa female germinal cell (egg) extract of pluricellular organisms inM-phase of the cell cycle.

To improve the entrance of the female germinal cell extract into thenuclei, the nuclear envelope can be permeabilized. The permeabilizationof the nuclei is achieved by the techniques well known in the art, suchas the use of a chemical agent, or a mild detergent, or an enzyme thatcan make small holes in the nuclear envelope, as lysolecithin, or via amechanical process which can at least partly open the nuclear envelope,for example pipetting.

The invention also relates to a composition comprising cells ofpluricellular organisms, possibly permeabilized, and a female germinalcell (egg) extract of pluricellular organisms in M-phase of the cellcycle.

To improve the entrance of the female germinal cell extract into thecells, the cell membrane can be permeabilized. The permeabilization ofthe cell membrane is achieved by the techniques well known in the art,such as the use of a chemical agent or a mild detergent, such asdigitonine, Triton, or an enzyme that can make small holes in the cellmembrane, as lysolecithin, or via a mechanical process which can atleast partly open the cell membrane, for example pipetting.

The present invention particularly relates to a composition as definedabove, wherein the cells of pluricellular organisms are differentiatedsomatic cells.

In a preferred embodiment of the invention, the invention relates to acomposition as defined above, wherein pluricellular organisms arevertebrates chosen among mammals, in particular humans, birds, reptilesand amphibians, and particularly Xenopus.

In another embodiment, the present invention relates to nuclei of cellsof pluricellular organisms, possibly permeabilized, containing a femalegerminal cell (egg) extract of pluricellular organisms in M-phase of thecell cycle.

According to the present invention, the nuclei can be used in a cellcontext or in an in vitro context, that is to say after extraction forthe cells. The nuclei can be extracted from the cells by the techniqueswell known in the art, such as cell breakage by incubation in ahypotonic buffer, use of a dounce homogenizer or a potter homogenizer oran isotonic buffer containing sucrose, glycerol or similar stabilizingagent and use of a potter homogenizer or dounce homogenizer able to openor disrupt the cell membrane.

The nuclei are stored in specific conditions to maintain theirintegrity, such as storage at −20° C., −80° C. or in liquid nitrogen inconditions known to be used to store oocytes or early embryos.

The present invention particularly relates to nuclei of cells ofpluricellular organisms, possibly permeabilized, which were reprogrammedby a female germinal cell (egg) extract of pluricellular organisms inM-phase of the cell cycle.

The term “reprogrammed” means that the nuclei of the cells haveundergone a mitotic remodeling, which conferred to the nucleus theability to adapt themselves to the early embryonic development.

The present invention particularly relates to nuclei of cells ofpluricellular organisms as defined above, which are nuclei of somaticdifferentiated cells.

In a preferred embodiment of the invention, the above-mentioned nucleiare nuclei of cells of vertebrates, chosen among mammals, in particularhumans, birds, reptiles and amphibians, and particularly Xenopus.

In another embodiment, the present invention relates to cells ofpluricellular organisms, possibly permeabilized, containing a femalegerminal cell (egg) extract of pluricellular organisms in M-phase of thecell cycle.

The present invention particularly relates to cells of pluricellularorganisms, possibly permeabilized, which were reprogrammed by a femalegerminal cell (egg) extract of pluricellular organisms in M-phase of thecell cycle.

The term “reprogrammed” means that the said nuclei of said cells haveundergone a mitotic remodeling, which conferred to the nucleus theability to adapt themselves to the early embryonic development.

The present invention particularly relates to cells of pluricellularorganisms as defined above, which cells are somatic differentiatedcells.

In a preferred embodiment, the invention relates to cells ofpluricellular organisms as defined above, which are cells ofvertebrates, chosen among mammals, in particular humans, birds, reptilesand amphibians, and particularly Xenopus.

The present invention also relates to a process for preparing nuclei asdefined above, wherein nuclei of cells of pluricellular organisms,possibly permeabilized, are in contact with a female germinal cell (egg)extract of pluricellular organisms in M-phase of the cell cycle, whichallows obtaining a mitotic remodeling of the chromosomes conferring tothe nucleus the ability to reproduce a replication phase characteristicof the early embryonic development.

The term “in contact” means that the nuclei and the female germinalextract are present together in suitable conditions, particularly in amedium comprising 10 mM HEPES pH 7.7, 100 mM KCl, 0.1 mM CaCl₂, 1 mMMgCl₂, 5% Sucrose, at a temperature preferably comprised from 20° C. to23° C., and preferentially for at least 45 minutes.

The invention also relates to a process for preparing cells as definedabove, wherein cells of pluricellular organisms, possibly permeabilized,are in contact with a female germinal cell (egg) extract ofpluricellular organisms in M-phase of the cell cycle, which allowsobtaining a mitotic remodeling of the chromosomes, conferring to thenucleus of said cells the ability to reproduce the early embryonicdevelopment.

The term “in contact” means that the cells and the female germinalextract are present together in suitable conditions, particularly in amedium comprising 10 mM HEPES pH 7.7, 100 mM KCl, 0.1 mM CaCl₂, 1 mMMgCl₂, 5% Sucrose, at a temperature preferably comprised from 20° C. to23° C., and preferentially for at least 45 minutes.

In another embodiment, the present invention relates to a process forcloning donor cells of pluricellular organisms comprising the followingsteps:

-   -   a female germinal cell (egg) extract of pluricellular organisms        in M-phase of the cell cycle is in contact with nuclei of donor        cells, possibly permeabilized, of non-human pluricellular        organisms intended for the cloning, or    -   with donor cells, possibly permeabilized, of non-human        pluricellular organisms intended for the cloning,    -   which allows a mitotic remodeling of the chromosomes of the        aforesaid donor cells,    -   the possible activation of the nuclei of the aforesaid donor        cells to trigger the S-phase of the cell cycle,    -   a possible step of partial or total remove of the female        germinal cell (egg) extract of pluricellular organisms,        particularly by washing the aforesaid nuclei or the aforesaid        donor cells,    -   the introduction of the nuclei or of the donor cells resulting        from the previous step in an enucleated egg.

In the context of the invention, the term “cloning” means obtaining anentire animal from the nuclei of a donor cell.

The nuclei of the donor cells can be activated to trigger the S-phase ofthe cell cycle, in order to initiate the first divisions of the earlyembryonic development. The activation may be achieved by the techniqueswell known in the art.

The female germinal cell (egg) extract can be partially or totallyremoved, particularly by washing the aforesaid nuclei or the aforesaiddonor cells, for example by several washings in Phosphate Buffer Saline(PBS).

The nuclei of the donor cells are introduced in an enucleated egg,according to the techniques well known in the art, such asmicroinjection.

For each enucleated egg, one nucleus or one donor cell is introduced.

The enucleated egg preferentially originates from the same species asthe nuclei. The enucleated egg is obtained by techniques well known inthe art.

The enucleated egg containing the nuclei can then be transferred in afemale breeder, so as to perform its early-embryonic, embryonic andfoetal development.

The present invention relates to a process as defined above, wherein thecells of pluricellular organisms are differentiated somatic cells orcells originating from different tissues of an organism.

Said cells originating from different tissues of an organism canparticularly be chosen among cells originating from any kind of tissue,such as skin, intestine, liver, blood, muscle, etc.

The present invention particularly relates to a process as definedabove, wherein the pluricellular organisms are vertebrates chosen amongmammals, birds, reptiles and amphibians, and particularly Xenopus.

The invention also relates to a process for preparing nuclei of cells ofpluricellular organisms, particularly vertebrates, comprising:

-   -   a step wherein nuclei of cells of pluricellular organisms,        particularly vertebrates, are in contact with a female germinal        cell (egg) extract of pluricellular organisms, particularly        vertebrates, in M-phase of the cell cycle, to obtain nuclei        containing the female germinal cell (egg) extract, said nuclei        being capable of reproducing the replication phases        characteristic of the early embryonic development, and    -   a step of partial or total remove of the aforesaid female        germinal cell (egg) extract.

In a particular embodiment, the invention relates to nuclei of cells ofpluricellular organisms, particularly vertebrates, as obtained by theimplementation of the above-mentioned process.

The present invention also relates to a process for preparing cells ofpluricellular organisms, particularly vertebrates, comprising:

-   -   a step wherein cells of pluricellular organisms, particularly        vertebrates, are in contact with a female germinal cell (egg)        extract of pluricellular organisms, particularly vertebrates, in        M-phase of the cell cycle, to obtain cells containing the female        germinal cell (egg) extract, the nuclei of said resulting cells        being capable of reproducing the replication phases        characteristic of the early embryonic development, and    -   a step of partial or total remove of the aforesaid female        germinal cell (egg) extract.

In another embodiment, the present invention relates to cells ofpluricellular organisms, particularly vertebrates, as obtained by theimplementation of the above-mentioned process.

The invention also relates to a process for obtaining multipotent ortotipotent stem cells of pluricellular organisms, particularlyvertebrates, comprising the following steps:

-   -   a female germinal cell (egg) extract of pluricellular organisms        in M-phase of the cell cycle is in contact with nuclei of donor        cells, possibly permeabilized, of non-human pluricellular        organisms, or    -   with donor cells, possibly permeabilized, of non-human        pluricellular organisms,    -   which allows a mitotic remodeling of the chromosomes of the        aforesaid donor cells,    -   the possible activation of the nuclei of the aforesaid donor        cells to trigger the S-phase of the cell cycle,    -   a possible step of partial or total remove of the female        germinal cell (egg) extract of pluricellular organisms,        particularly by washing the aforesaid nuclei or the aforesaid        donor cells,    -   the introduction of the nuclei or of the nuclei of the donor        cells resulting from the previous step in an enucleated egg,    -   a step of culturing the resulting nucleated egg in appropriate        conditions for several divisions, to obtain multipotent or        totipotent stem cells, and    -   a possible step of culturing the resulting multipotent or        totipotent stem cells in appropriate conditions to maintain said        cells in an undifferentiated state.

The resulting multipotent or totipotent stem cells can be cultured inappropriate conditions to maintain said cells in an undifferentiatedstate.

In another embodiment, the invention relates to a process for obtainingmultipotent or totipotent stem cells of pluricellular organisms,particularly vertebrates, comprising:

-   -   a step wherein permeabilized donor cells of pluricellular        organisms, particularly vertebrates are in contact with a female        germinal cell (egg) extract of pluricellular organisms,        particularly vertebrates, in M-phase of the cell cycle, or    -   with an extract of non-human early embryos of vertebrates,    -   to obtain a mitotic remodeling of the chromosomes of the        aforesaid cells and to obtain the aforesaid donor cells as        multipotent or totipotent cells,    -   a possible step of partial or total remove of the aforesaid        female germinal cell (egg) extract or of the aforesaid embryo        extract,    -   a possible step allowing to close up the membrane of the        aforesaid multipotent or totipotent cells, and    -   a possible step of culturing the aforesaid resulting multipotent        or totipotent stem cells in appropriate conditions to maintain        said cells in an undifferentiated state.

The donor cells are preferentially lightly permeabilized.

“Lightly permeabilization” is obtained for example by using lowconcentrations of detergent like NP40, Triton X100, Lysolecithin,digitonin.

By the expression “extract of non-human early embryos of vertebrates”,it is meant an extract such as obtained by the process described inLemaitre et al. 1998.

The invention particularly relates to a process for obtaining cells,cellular lines or tissues of pluricellular organisms, particularlyvertebrates, at the desired stage of differentiation, comprising:

-   -   a step wherein permeabilized donor cells of pluricellular        organisms, particularly vertebrates are in contact with a female        germinal cell (egg) extract of pluricellular organisms,        particularly vertebrates, in M-phase of the cell cycle, or    -   with an extract of non human early embryos of vertebrates,    -   to obtain a mitotic remodeling of the chromosomes of the        aforesaid donor cells and to obtain the aforesaid donor cells as        multipotent or totipotent cells,    -   a possible step of partial or total remove of the aforesaid        female germinal cell (egg) extract or of the aforesaid embryo        extract,    -   a step allowing to close up the membrane of the aforesaid        multipotent or totipotent cells, and    -   a step of culturing the aforesaid resulting multipotent or        totipotent stem cells in appropriate conditions to obtain cells,        cellular lines or tissues, at the desired stage of        differentiation.

The invention also relates to cells, cellular lines or tissues asobtained by the implementation of the above defined process.

The Inventors have investigated the factors that control the ability ofdifferentiated adult cell nuclei to participate in early developmentalevents when transplanted into eggs or egg extracts. In particular, theInventors show that mitosis is crucial for resetting the nuclearorganization of differentiated nuclei and for adapting them for theaccelerated DNA replication of early embryos. In both metaphase-arrestedXenopus egg extracts and at mitosis of early embryonic cycles, theformation of mitotic chromosomes is a necessary step in organizing DNAfor subsequent replication. Incubating differentiated adult nuclei in amitotic extract shortens the average size of replicons and chromatinloop domains to those typical of endogenous chromatin present duringearly development. Molecular DNA combing demonstrates that a singlemitosis is both necessary and sufficient to reset inter-origin spacing.This reprogramming of replicon organization is topoisomeraseII-dependant, and results in an increased recruitment of replicationfactors to origins that is not simply a function of the amount ofavailable pre-replication complex proteins. Finally, the Inventors showthat an equivalent remodeling of the chromatin occurs at mitosis of eachcell cycle during early development. These results can explain how theegg is able to remodel differentiated nuclei, and why cloningexperiments by nuclear transfer of differentiated nuclei have such ahigh failure rate.

FIGURES

FIG. 1: Exposure to N-phase conditions makes erythrocyte nuclei fullycompetent for DNA replication

FIG. 1A: Scheme of the experimental procedure described in the text.

FIG. 1B: Permeabilized erythrocyte nuclei were incubated in S-phase orM-phase extract for 45 minutes before CaCl₂ activation to trigger Sphase. 5 μl samples were taken at different times. DNA replication wasmonitored by TCA precipitation of ³²PαdCTP incorporated into DNA andexpressed as the percentage replicated DNA compared to the total inputDNA. Sperm nuclei incubated in S-phase extract were used as a control.Other independent experiments show that permeabilization was notnecessary when erythrocyte nuclei are incubated in M-phase extracts.

FIG. 1C: Replication initiation foci were analyzed in erythrocyte nucleiby incorporating Biotin16-dUTP in the presence of 5 μg/ml aphidicolin,as indicated, in S-phase extract or in M-phase extract for 45 minutesbefore CaCl₂ activation. DNA was stained with Hoechst 33258. The RPAantibody was revealed with an anti-mouse FITC, and Biotin-16 dUTP withstreptavidin Texas red.

FIG. 2: Single molecule analysis of the inter origin spacing bymolecular combing.

Sperm nuclei (FIG. 2A) and permeabilized erythrocytes nuclei (FIG. 2B)were incubated for 75 min in S-phase extract supplemented with 5 μg/mlaphidicolin and 40 μM BrdUTP. Erythrocyte nuclei (FIG. 2C) and spermnuclei (FIG. 2D) were first incubated in M-phase extract for 45 minbefore CaCl₂ activation and addition of aphidicolin.

Fibers were combed on silanized coverslips and the center to centerdistances between adjacent BrdU tracks were measured. The center tocenter distance between BrdU tracks is indicated in Kbp. Lower panel,BrdU; upper panel, merge BrdU/DNA.

FIG. 3: Histone acetylation does not induce erythrocyte nucleiremodeling.

FIG. 3A: Sperm nuclei were incubated in S-phase extract in the presenceof histone acetylation activators (300 μM TSA and 300 μM CTPB).

FIG. 3B: Sperm nuclei were incubated in S-phase extract in the presenceof a histone acetylation inhibitor (300 μM AA). A prior incubation of600 μM CTPB was necessary to prevent inhibition of DNA replication by300 μM AA.

FIG. 3C: Permeabilized erythrocyte nuclei were incubated in S-phaseextract containing either 300 μM TSA, 600 μM CTPB, or 300 μM AA. Spermnuclei incubated in S-phase extract were used as a control.

FIG. 3D: Transfer of sperm and erythrocyte chromatin from a 45 minincubation in M-phase extract to S-phase extract containing 300 μM AA.

5 μl samples were taken at different times and DNA replication wasmonitored by TCA precipitation of ³²PαdCTP incorporated into DNA.

FIG. 4: Mitosis-induced remodeling of nuclear organization

FIG. 4A: Erythrocyte nuclei were incubated either in S-phase or M-phaseegg extract or mock incubated. The nuclear matrix-associated DNA waspurified using the LIS procedure and the DNA fragments remaining on thematrix were ³²P-labelled and used to probe specific regions of the rDNAdomain.

FIG. 4B: A plasmid containing the Xenopus rDNA domain was cut withHindIII, EcoRI, and XbaI to produce five fragments. Fragment 1 is theintergenic spacer element between the rDNA units, Fragments 2, 3 and 4are within the transcription unit, and Fragment 5 is the vectorsequence.

FIG. 4C: DNA fragments were separated by agarose gel electrophoresis andstained with Ethidium Bromide (first gel) or transferred to nylonmembranes for hybridization. Total Xenopus DNA often partly hybridizeswith one of the plasmid bands (second gel), as does thematrix-associated DNA from erythrocytes incubated in M-phase extract(fifth gel), emphasizing the random nature of this fraction. Hybridationof the rDNA digest with matrix attachment fraction is shown fromerythrocytes incubated (4) or not (3) in S-phase egg extract.

FIG. 4D: Nuclei were recovered on coverslips and submitted to themaximum fluorescent halo technique (MFHT) for DNA loop size measurements(Material and Methods).

FIG. 4E: Ethidium bromide was used to stain DNA loops as in FIG. 4D,while immunostaining with anti-lamin antibody was also used todelimitate matrix and loop fractions.

FIG. 4F: The method was applied to both sperm nuclei and erythrocytenuclei in interphase that had been previously incubated for 45 min inM-phase egg extract. Histograms show individual loop size measurements.

FIG. 5: ORC binding and DNA replication efficiency depends on thechromatin context and on topoisomerase II activity.

FIG. 5A: Erythrocyte chromatin was incubated either in M-phase extractand immediately driven into S phase by Ca⁺⁺, or in M-phase extract for45 min before induction into S phase by Ca⁺⁺ in the absence or presenceof ICRF. Control sperm chromatin in M-phase extracts induced to enter Sphase by calcium is shown. The amount of nuclei was 1000 nuclei/μl eggextract for sperm nuclei, and 500 nuclei/μl egg extract for erythrocytenuclei to keep the chromatin concentration constant.

FIG. 5B: Demembranated erythrocyte nuclei or sperm nuclei were incubatedin a mitotic egg extract in the presence or absence of 50 μg/ml of thetopoisomerase II inhibitor ICRF193. DNA was stained with Hoechst dye forchromosome formation analysis.

FIG. 5C: Chromatin was purified and proteins analyzed by SDS gelelectrophoresis as described in Material and Methods. Erythrocyte nuclei(500 nuclei/μl egg extract) or sperm nuclei (1000 nuclei/μl egg extract)were incubated in a mitotic egg extract, induced to enter S phase withcalcium, in the presence (+) or absence (−) of ICRF 193. Chromatin waspurified 30 min after calcium activation and analyzed by immunoblot witha Xenopus anti ORC2 antibody.

FIG. 5D: Sperm nuclei and erythrocyte nuclei were incubated for 30 minin S-phase extract at various DNA concentrations. Chromatin was purifiedand analyzed by 10% SDS PAGE by immunoblot with a Xenopus anti ORC2antibody.

FIG. 5E: Quantitation from the immunoblot of FIG. 5D.

FIG. 6: Cell cycle remodeling of chromatin organization in early Xenopusembryos.

FIG. 6A: Karyomeres form at the anaphase-telophase transition andinitiate DNA replication before nuclei are reconstructed (Lemaitre etal, 1998). DNA was stained with Hoechst 33258 and embryonic nuclei atanaphase (a), telophase (b) and after replication (c) are shown.

FIG. 6B: Nuclei from early embryos were isolated and treated with DNaseI. The nuclear matrix was prepared using the LIS procedure (Materialsand Methods) and the DNA fragments remaining on the matrix were32P-labelled and used to probe for specific regions of the rDNA domainas in FIG. 4. The fragments were separated by agarose gelelectrophoresis and stained with Ethidium bromide, or transferred tonylon membranes and hybridized either with total Xenopus DNA probe orwith nuclear matrix DNA from karyomeres or early embryonicpost-replicative nuclei.

FIG. 6C: Nuclei were recovered on coverslips and submitted to themaximum fluorescent halo technique (MFHT). Histograms show individualloop size measurements.

FIG. 7: Mitotic remodeling of chromatin loop domains occurs in S andM-phases.

FIG. 7A: Sperm nuclei or post-replicative nuclei were incubated inS-phase extract in the presence of ³²PαdCTP. 5 μl samples were taken atdifferent times and DNA replication was quantitated by TCAprecipitation.

FIG. 7B: The length of nascent DNA strands analyzed by 0.8% agarosealkaline gel electrophoresis The position of molecular weight markers(MW) run in parallel is indicated.

FIG. 7C: Sperm nuclei collected at different times during replication orfollowing M-phase were recovered on coverslips and submitted to MFHT forDNA loop size measurements. Entry into mitosis was induced by incubatingpost-replicate embryo nuclei in M-phase extract in the presence orabsence of ICRF.

FIG. 7D: Distribution of loop sizes.

FIG. 8: Cell cycle remodeling of chromatin organization in the earlyXenopus embryo.

Reorganization of chromatin occurs with each cell cycle and is dependenton Topo II activity. During S-phase, fusion of replicons leads to anincrease in the mean DNA loop size. These large loops are remodeled intosmall loops at each mitosis and permit an increased binding of ORC for ahigher rate of DNA replication. Border (dark) and internal (light) boxesof FIG. 8 represent both potential loop attachment sites and replicationorigins.

FIG. 9: Pre-RC proteins and nucleosome assembly in M-phase.

FIG. 9A: One microliter of extract was loaded onto a 10% SDS PAGE andtransferred for immunoblotting with ORC1, ORC2, MCM3 and MCM4antibodies. Note the dephosphorylation of MCM4 at mitosis exit, aspreviously described (Coue et al., 1996).

FIG. 9B: Chromatin assembled in M-phase or S-phase extract was purifiedas described in Materials and Methods and analyzed for ORC1, ORC2, MCM4,and MCM3 binding.

FIG. 9C: Nucleosome spacing assay: Chromatin was purified fromerythrocytes, incubated either in S-phase extract or for 45 min inM-phase extract before S-phase triggering with CaCl₂, and resuspended inmicrococcal digestion buffer containing 0.3% Triton X-100 and 3 mMCaCl₂. Chromatin digestion was initiated by adding 60 U micrococcalnuclease, as described (Almouzni and Mechali, 1988), and DNA productswere analyzed by 1.8% agarose gel electrophoresis. A ladder ofnucleosomes was observed in both cases.

FIG. 10: Chromatin organization in the rDNA domain revealed using DNAarrays.

A recently-developed method for mapping the interactions of DNA with thenuclear matrix based on oligonucleotide DNA arrays (Ioudinkova et al.,2005) was used to confirm the results presented in FIG. 4.

FIG. 10A: rDNA gene domain. Numbered blocks indicate the positions ofthe oligonucleotides within the array.

FIG. 10B: The graphs represent the hybridization ratios of nuclearmatrix-associated DNA normalized against an internal oligonucleotideno. 1. The average of two independent experiments is presented. TotalXenopus DNA hybridized equally to the rDNA array, suggesting that thechosen oligonucleotides do not contain external DNA repeats.

FIG. 11: Erythrocyte remodeling does not occur during the transitionfrom M to S phase. Erythrocytes nuclei were incubated for 45 min inM-phase extract and chromatin purified without previous activation ofthe M-phase extract. It was then directly transferred to S-phaseextract. DNA replication was measured by a 3 hours incubation in S-phaseextract in the presence of ³²PαdCTP. The first control corresponds tothe level of replication obtained with erythrocyte incubated in the sameconditions in M-phase extract during 45 min and ca2+ activated totrigger S phase. The second control corresponds to the level ofreplication of erythrocytes nuclei incubated directly in S-phase extractwithout M-phase remodeling.

FIG. 12: Topo II depletion in M-phase extract prevents mitoticremodeling of erythrocyte nuclei

FIG. 12A: Depletion of TopoII in M-phase was carried out using ananti-TopoII polyclonal antibody kindly provided by Dr. Bogenhagen.Depletion was monitored by immunoblot.

FIG. 12B: Erythrocyte nuclei and sperm nuclei were incubated in adepleted M-phase extract for 45 min and S-phase was triggered byaddition of CaCl₂. DNA replication was measured after 3 hours ofincubation. A mock depletion was also performed using a non-specificrabbit IgG.

FIG. 13: Topo II inhibition of S phase extracts by ICRF193 does notinterfere with DNA replication

Sperm chromatin was incubated in S-phase extract in the presence of 50μg/ml ICRF193 at the beginning of the reaction or after 45 min (duringthe elongation phase). DNA replication was monitored by TCAprecipitation of the replicated DNA.

FIG. 14: Replicon and ORC2 binding in sperm nuclei or post-replicativeembryonic nuclei.

FIG. 14A: Demembranated post-replicative embryonic nuclei ordemembranated sperm nuclei were incubated in S-phase extract. Chromatinwas purified and proteins analyzed by SDS gel electrophoresis asdescribed in Material and Methods.

FIG. 14B: Quantitation from the immunoblot.

EXAMPLES Example 1 Mitotic Remodeling of Replicon

Nuclear transfer experiments frequently fail due to the inability ofmost transplanted nuclei to support normal embryonic development. TheInventors show here that the formation of mitotic chromosomes in the eggcontext is crucial for adapting differentiated nuclei for earlydevelopment. Fully-differentiated erythrocyte nuclei replicateinefficiently in Xenopus eggs, but do so as rapidly as sperm nuclei if aprior single mitosis is permitted. Formation of chromosomes is necessaryand sufficient to reset erythrocyte nuclei to short inter-origin spacingcharacteristic of early developmental stages. This resetting involves ashortening of chromatin loop domains and an increased recruitment ofreplication initiation factors onto chromatin, leading to a largeincrease in replication origins. Finally, the Inventors show that thismitotic remodeling is topoisomerase II dependent, occurs with each earlyembryonic cell cycle, and dominantly regulates the initiation of DNAreplication at the subsequent S phase. These results indicate thatmitotic conditioning is determinant to reset chromatin structure ofdifferentiated adult donor cells for embryonic DNA replication, andsuggest that it is an important step in nuclear cloning.

Material and Methods

Xenopus Egg Extracts and Early Embryos

S-Phase and M-phase low speed (LS) extracts were prepared according toprotocols described in detail by (Menut et al., 1999) and available atwww.igh.cnrs.fr/equip/mechali/. Embryos were grown in 0.1× Barth'smedium as described (Lemaitre et al., 1995). To obtain karyomeres,perfectly synchronized embryos were selected at each division over thefirst four divisions. Embryos were then taken at the fifth division whenthe furrow appears. Subsequent divisions give rise to metasynchronousdivisions in the embryos. G2-like synchronized embryos were obtained by45 min incubation in 0.1× Barth's medium containing 150 μg/mlcycloheximide between the 32- and 64-cell stages and between the 512-and 1,024-cell stages. Embryos were dejellied with 2% cysteine HCl, pH7.9, and homogenized through a 1-ml Gilson tip before centrifuged at 4°C. for 10 min at 10,000 g. Under these conditions, the endogenousembryonic nuclei (karyomere or reformed nuclei) remain in thesupernatant (Lemaitre et al., 1998).

Replication Reactions

Demembranated sperm nuclei were prepared and used as described in (Menutet al., 1999), and erythrocyte nuclei were purified from Xenopus bloodas described. Nuclei were incubated in S-phase (1,000 nuclei/μl), orM-phase (CSF) extracts that were activated with 1 mM CaCl₂. DNAsynthesis was measured by ³²P-dCTP incorporation, as previouslydescribed (Menut et al., 1999).

Purification and Analysis of Chromatin Fractions

50 μl samples were diluted with 5 volumes of extract buffer (XB: 100 mMKCl, 0.1 mM CaCl₂, 1 mM MgCl₂, 10 mM KOH-Hepes pH 7.7, 50 mM sucrose)and pelleted by centrifugation at 7500 g for 12 min through a 0.7 Msucrose cushion. Nuclear pellets were resuspended in XB, 0.3% TritonX-100 and incubated for 5 min on ice. After a further 5,000 gcentrifugation for 5 min, chromatin pellets were recovered and adjustedin Laemmli Buffer.

Antibodies

Lamins were visualized with the 687A7 antibody (Firmbach-Kraft andStick, 1995). The anti-RPA34-specific monoclonal antibody (324A.1) wasused as described (Francon et al., 2004). The rabbit polyclonal antibodyagainst Cdc6 was produced as described (Lemaitre et al., 2002).Antibodies against Cdt1 and MCM4 were obtained by four injections ofcorresponding recombinant proteins. Other antibodies were generous giftsfrom J. Walter (ORC2), and D. Bogenhagen (TopoII)

Immunocytochemistry

Extracts containing nuclei were diluted 10-fold in 100 mM KCL, 50 mMsucrose, 5 mM MgCl₂, 0.5 mM EDTA, 20 mM Hepes pH 7.6, and nuclei werepurified through a 0.7 M sucrose cushion. Alternatively, samples weredirectly fixed with an equal volume of XB containing 4% formaldehyde and1 μg/ml Hoechst 33258. Rehydration was done in PBS. Isolated nuclei wereincubated for 1 hour at room temperature in PBS 2% BSA, 0.1% Tween 20 toblock non-specific interactions. Incubation with specific antibodies wascarried out overnight at 4° C. in PBS, 2% BSA. After several washes, thesecond FITC-conjugated or Texas Red-conjugated streptavidin was addedfollowing instructions from the manufacturers. To reveal Biotin dUTP,FITC or Texas Red conjugated-streptavidin was mixed with the secondantibody at the appropriate dilution. DNA was stained with 1 μg/mlHoechst 33258.

DNA Combing

Nuclei embedded in agarose plugs (800 ng DNA/plug) were stained withYOYO-1 (Molecular Probes) and resuspended in 50 mM MES pH 5.7 (150ng/ml) after digestion of the plugs with agarase (Roche). DNA combingwas performed as described (Michalet et al., 1997). Combed DNA fiberswere denatured for 30 min with 1 N NaOH and BrdU was detected with a ratmonoclonal antibody (Sera Lab) and a secondary antibody coupled to Alexa488 (Molecular Probes). DNA molecules were counterstained as previouslydescribed (Versini et al., 2003) with an anti-guanosine antibody(Argene) and an anti-mouse IgG coupled to Alexa 546 (Molecular Probes).Center-to-center distances between BrdU tracks were measured withMetaMorph (Universal Imaging Corp.) using adenovirus DNA molecules as asize standard (1 pixel=680 bp).

Loop Size Measurement

Maximum Fluorescent Halo Radius (MFHR) were determined by treatingnon-fixed nuclei on coverslips. They were first dipped for 1 min in icecold NP40 buffer (0.5% NP40, 10 mM MgCl₂, 0.5 mM CaCl₂, 50 mM Hepes pH7.8) and then sequentially dipped for 30 s in a solution containing 0.2mM MgCl₂, 10 mM Tris (pH 7.4) with 0.5 M, 1 M, 1.5 M, 2 M NaCl. Theywere then incubated in 100 μg/ml ethidium bromide, 2 M NaCl and exposedfor 1 min to short wave UV light before observation by fluorescence(Buongiorno-Nardelli et al., 1982). Halo and matrix diameters wereestimated using a micrometrics slide. DNA loop size was calculatedtaking into account that the loop size is 2 fold the MFHR. The length oflinear DNA was calculated using the correspondence of 1 μm to 2.3 kbp.

Analysis of DNA Loop Attachments Sites

Nuclear matrices were prepared by treating isolated nuclei withrestriction endonucleases or DNase I followed by extraction with eitherLithium 3,5-diiodosalicylate (LIS) or 2 M NaCl, essentially as describedin (Gasser and Laemmli, 1986; Vassetzky et al., 2000). Nuclei weredigested with 100 μg/ml DNaseI for 3 h at 0° C. in (100 mM NaCl, 25 mMKCl, 10 mM Tris-HCl, pH 7.5, 0.25 mM spermidine, 1 mM CaCl₂). Thedigestion was followed by a stabilization step, the addition of CuCl₂ toa final concentration of 1 mM, and incubation for 10 min at 4° C. Thenuclei were extracted with five volumes of LIS extraction buffercontaining 10 mM Tris-HCl, pH 7.5, 0.25 mM spermidine, 2 mM EDTA-KOH, pH7.5, 0.1% digitonin, and 25 mM LIS for 5 min at room temperature. Thehistone-depleted nuclear matrices were recovered by centrifugation at2,500 g for 20 min at room temperature, and the nuclear matrix pelletwas washed three times in 20 mM Tris-HCl, pH 7.5, 0.25 mM spermidine,0.05 mM spermine, 100 mM NaCl, and 0.1% digitonin. The size range of thenuclear matrix-attached DNA was 400-1500 bp.

Oligonucleotide DNA Array

The array was devised to use the complete Xenopus rDNA sequence,assembled from entries X05264 and X02995 (Genbank) and comprising 11505base pairs. The micro-array consisted of seven oligonucleotides spacedapproximately 1500 bp apart (see Table 1) and possessing similar sizes(25-30 bp) and annealing temperatures (60±1°). The first twooligonucleotides covered the intergenic spacer and the other fivespanned the 40S transcript.

The oligonucleotides were slot-blotted onto Zeta-probe GT filters in 0.4NaOH and fixed by baking at 80° C. for 30 min. Each filter contained thearray in duplicate. The hybridization was carried out at 58° C. inmodified Church buffer (0.5 M phosphate buffer pH 7.2, 7% SDS, 10 mMEDTA) overnight. The blot was subsequently washed in 2×SSC, 0.1% SDStwice for 5 min, and then in 1×SSC, 0.1% SDS, twice for 10 min andexposed on a PhosphoImager. All experiments were done in duplicate. Thedata has been normalized versus an internal control (oligonucleotide No.1).

TABLE 1   Annealing temper- Posi- Size, ature, tion Oligonuoleotide nt °C.  1476 GGAGAGGTAGAGACAAGACAGAGGC 25   60.3 (SEQ ID NO: 1)  2723GGGCGAAGAAAACCGGGAGAAATAC 25   60.8 (SEQ ID NO: 2)  4136GAGAGAAAGACGGAAAGAAAGGAGAGTAG 29 60 (SEQ ID NO: 3)  5279CATTCGTATTGTGCCGCTAGAGGTG 25   60.7 (SEQ ID NO: 4)  7181CCACGACTCAGACCTCAGATCAGAC 25   60.8 (SEQ ID NO: 5)  8829GTAACAACTCACCTGCCGAATCAACTA 27   60.3 (SEQ ID NO: 6) 10262CTGTGAAGAGACATGAGAGGTGTAGGATAA 30   60.9 (SEQ ID NO: 7)

Results

Reprogramming Differentiated Nuclei for DNA Replication Requires PassageThrough Mitosis

When sperm nuclei are introduced into Xenopus interphase egg extracts,they replicate almost immediately and with an efficiency of close to100%, similar to what happens in vivo following fertilization (Blow andLaskey, 1986). In contrast, erythrocyte nuclei replicate inefficiently(Leno and Laskey, 1991; Lu et al., 1999). Both human and Xenopus eggsare normally blocked at the stage of the second meiotic division withcondensed chromosomes at the metaphase stage (Tunquist and Maller,2003), and fertilization induces a calcium pulse that triggers the endof mitosis and the onset of embryonic cleavage. However, whendifferentiated nuclei are transplanted into eggs, microinjection inducesan immediate exit from mitosis and thereby prevents differentiatednuclei from undergoing mitotic chromosome condensation prior to passageinto post-mitotic cell cycle phases.

The Inventors asked whether passage through mitosis might be aprerequisite for reprogramming the nucleus for rapid DNA replication.The experimental procedure outlined in FIG. 1A was used. Erythrocytenuclei were either permeabilized and directly incubated in XenopusS-phase extracts, or incubated in a mitotic egg extract beforeactivation in S phase. The Inventors observed that permeabilizederythrocyte nuclei replicate less efficiently in S-phase egg extractsthan do permeabilized sperm nuclei (FIG. 1B). When permeabilizederythrocyte nuclei were first, however, incubated in an M-phase extractprepared from eggs blocked at the second meiotic metaphase by EGTA(Murray, 1991) prior to S phase induction using CaCl₂, replicationoccurred as rapidly and efficiently as in sperm nuclei (FIG. 1B). TheInventors confirmed that chromosomes were formed before the Ca²⁺ wasadded in each experiment (data not shown and FIG. 5A). In other words,the formation of chromosomes by an initial exposure to mitoticconditions made erythrocyte nuclei as competent for DNA replication assperm chromatin. As previously seen with sperm chromatin (Adachi andLaemmli, 1992), erythrocyte DNA replication occurred in focicolocalizing with RPA (FIG. 1C); the Inventors observed an increasednumber of such foci when erythrocyte chromatin was allowed to first passthrough mitosis.

M-Phase Extract Conditioning Increases Number of Replication Origins

While DNA replication initiates at origins spaced every 10 to 20 Kbpduring early Xenopus development, permitting a high rate of replication(Hyrien and Mechali, 1993; Walter and Newport, 1997), in most dividingsomatic cells the replicon size ranges from 50 to 300 Kbp (Berezney etal., 2000). To address whether mitotic remodeling of erythrocyte nucleiaffects replicon size, the Inventors analyzed the spacing of origins byDNA combing (Michalet et al., 1997). In this method, DNA molecules arestretched uniformly, providing an accurate determination of origindensity along the DNA (Pasero et al., 2002). Erythrocyte nuclei wereincubated in egg extracts in the presence of BrdUTP, which labelsinitiation sites, and a low concentration of aphidicolin, which permitsinitiation but slows elongation dramatically (Walter and Newport, 2000;Wu et al., 1997; and unpublished results of the Inventors). ChromosomalDNA was purified and combed on silanized glasses, BrdU incorporationdetected using anti-BrdU antibodies, and DNA fibers counter-stained withan anti-guanosine antibody. FIG. 2A shows that sperm nuclei had anaverage spacing of 23.4 Kbp between replication origins, while thespacing for erythrocyte nuclear chromatin incubated in S-phase eggextract ranged from 30 to 230 Kbp (FIG. 2B). 77% of the replicons weresmaller than 30 Kbp in the Xenopus nuclei, whereas 97% of the repliconswere larger than 30 Kbp in the erythrocyte nuclei. The Inventorsconclude that the slow replication observed in erythrocyte nuclei thathad been exposed to S-phase extract was due to a low frequency ofreplication initiation within the genome.

When erythrocyte nuclei were first exposed to M-phase extract beforeentry into S phase, however, the spacing of origins was shortened to24.9 Kbp, similar to sperm nuclei (FIG. 2C). The proportion of repliconslarger than 30 Kbp was dramatically decreased, with 74% of the repliconsbeing in the 10-30 Kbp range. Finally, incubation of sperm nuclei in anM-phase extract prior to S phase had no effect on origin spacing (FIG.2D). The Inventors conclude that prior conditioning of erythrocytenuclei in M-phase extract set an origin spacing similar to those ofsperm chromatin upon entry into S phase.

Mitotic Remodeling is not Due to Global Changes in NucleosomeOrganization Nor to Histone Acetylation Levels

Although the above results could suggest a superior ability of M-phaseextract to assemble proteins of the pre-replication complex, theInventors doubted this possibility for two reasons. First, M-phaseextracts do not contain higher levels of pre-replication complexproteins than do interphase egg extracts (Supplementary FIG. 1A andunpublished results). Second, several of the proteins do not bind tochromatin during mitosis, including ORC, CDC6, Cdt1, RPA, and MCMs(Supplementary FIG. 1B).

An alternative explanation is that building mitotic chromosomalstructures is sufficient to reset the nuclear organization oferythrocyte nuclei for DNA replication in the next cell cycle. To testthis possibility, the Inventors first examined nucleosome assembly andspacing in the nuclei. As shown in Supplementary FIG. 1C, the globalnucleosome organization was similar regardless of whether the nucleiwere added directly to the S-phase extract or were first incubated in anM-phase extract.

The Inventors also investigated whether the level of histone acetylationcould account for their results, particularly in view of the recentsuggestion that acetylation may contribute to the specification ofreplication origins (Aggarwal and Calvi, 2004; Danis et al., 2004).Histone acetylation is determined by the equilibrium between theactivities of histone acetyl transferases (HATs) and histonedeacetylases (HDACs), both of which are present in Xenopus oocytes (Ryanet al., 1999; Wade et al., 1999). This equilibrium can be modified infavor of acetylation either by inhibiting deacetylases with trichostatin(TSA) or by activating acetylases with CTPB. Conversely, histonedeacetylation can be promoted by inhibiting histone acetylases withanacardic acid (AA) (Balasubramanyam et al., 2003). FIG. 3A shows thatfavoring acetylation (TSA or CTPB) had no significant effect on thereplication rate of sperm chromatin incubated in S-phase extract. Theseresults indicated either that histone acetylation is not necessary forDNA replication of sperm nuclei, or that the level of acetylationpresent in the extract is sufficient to allow a maximum rate ofreplication. FIG. 3B shows that the latter possibility is more likely,as AA, which causes hypoacetylation of H3 and H4, strongly inhibited thereplication of sperm nuclei in S-phase extract. This inhibition could bereversed by the activator CTPB. These results clearly indicate thathistone acetylation is required for the rapid replication seen duringearly development, and that the steady-state level of acetylationactivity in the egg is sufficient for a maximum rate of DNA replication.

As with sperm chromatin, the acetylation activators TSA and CTPB failedto significantly affect the replication rate of erythrocyte nucleiincubated in S-phase extract (FIG. 3C). Unlike with sperm chromatin,however, the acetylase inhibitor AA did not further inhibit theinefficient DNA replication of erythrocyte nuclei. Erythrocyte nucleithat had been remodeled in mitosis, however, were as sensitive as spermnuclei to AA (FIG. 3D). Together, these data suggest, first, thatalthough acetylation is required for the rapid DNA replicationcharacteristic of early S phases, its level is sufficient for a fullrate of DNA replication and therefore cannot account for the slow DNAreplication rate observed with erythrocyte nuclei in interphasicextracts. Second, they indicate that the organization of erythrocytechromatin negatively regulates DNA replication in a dominant manner in Sphase extracts, unless mitotic chromosomes are first formed byincubation in an M-phase extract.

Mitotic Reorganization of Erythrocyte Chromatin Domains

The Inventors next investigated global changes in the organization oferythocyte chromatin that could explain replicon remodeling. Atransition from a random association with the nuclear matrix to adefined anchorage occurs during Xenopus development as chromatin domainsbecome organized for transcription after the Mid Blastula transition(Vassetzky et al., 2000). The Inventors hypothesized that the reversecould take place when erythrocyte nuclei are exposed to egg extracts. Totest this, nuclei incubated in M-phase extracts, S-phase extracts, ormock incubated, were treated with DNase I and then extracted with LIS,which removes histone and non-histone proteins but preserves theattachment sites of DNA loops to the nuclear scaffold (FIG. 4A). The DNAremaining on the matrix was isolated, labeled, and used as a probe tohybridize to agarose gel-separated regions of the rDNA domain (FIGS. 4B,4C). The gels were also probed with total Xenopus erythrocyte DNA (FIG.4C).

Each unit of the rDNA domain comprises a transcribed region and anon-transcribed spacer. A single band corresponding to the intergenicspacer was detected when matrix-associated erythrocyte DNA was used as aprobe, whereas all rDNA bands were detected when total Xenopuserythrocyte DNA was used (FIG. 4C). While exposing erythrocyte nuclei toS-phase egg extract did not significantly alter the rDNA specificity,incubation in an M-phase egg extract produced a randomization of theattachment sites, as all rDNA domains were detected with similarefficiency (FIG. 4C). The Inventors obtained analogous results with adifferent method using oligonucleotide arrays. Nuclear matrix DNA fromerythrocytes only hybridized to the two oligonucleotides correspondingto the intergenic spacer, confirming the results of FIG. 4. Incubationof erythrocyte nuclei in S-phase extract did not alter the hybridizationpattern. Incubation of erythrocyte nuclei in mitotic extracts led to ahybridization pattern similar to that of total DNA, suggesting a lack ofspecific locus attachment sites. Inhibition of DNA topoisomerase II inthe M-phase extract or, to a lesser extent, depletion of DNAtopoisomerase II with specific antibodies, maintained the originalorganization of the rDNA gene domain.

To try to explain these results, the Inventors investigated whethermitosis affects the density of the loop attachment sites within the rDNAdomain. The chromatin loop sizes were measured using the “MaximumFluorescent Halo Technique” (Vogelstein et al., 1980). In this method,nuclei were first treated with high salt and then briefly irradiatedwith UV in the presence of ethidium bromide, which causes extended DNAloops to form a fluorescent halo around the residual nuclear structure(FIG. 4D and Materials and Methods). The loop size was estimated basedon the diameter of the fluorescent halo (Buongiorno-Nardelli et al.,1982; Vogelstein et al., 1980), which could be distinguished from theresidual nucleoskeleton by immunolocalization of the nuclear lamina(FIG. 4E). FIG. 4F, panel (a), shows that erythrocyte nuclei have a meanloop size of 97.1+/−6.8 kbp, similar to what is seen in other somaticcell nuclei (data not shown and (Buongiorno-Nardelli et al., 1982;Vogelstein et al., 1980)). While this size did not change when nucleiwere permeabilized and incubated in S-phase egg extracts (FIG. 4F, b),exposure to an M-phase egg extract prior to calcium activation causedthe loop size to decrease to 15.4+/−3.1 kbp (FIG. 4F, c), close to thevalue of sperm nuclei or early embryonic nuclei in S-phase (FIG. 4F, d,and FIG. 6C).

The Inventors conclude that passage through M-phase prior to S phaseinduction induces two kinds of rearrangements in erythrocyte nuclei:First, it reduces the loop size, consistent with a higher density ofanchorage sites to the nuclear matrix. Second, it decreases the averagespacing of replication origins in parallel proportions. In both cases,the organization of chromatin domains becomes similar to that of spermnuclei entering S phase.

Topoisomerase II is Involved in Replicon Resetting at M Phase.

Since introducing sperm chromatin into mitotic egg extracts causes thechromosomes to condense (Lohka and Masui, 1983), the Inventors nextinvestigated whether chromosome condensation, driven by topoisomerase IIin Xenopus M-phase egg extracts (Adachi et al., 1991; Wood and Earnshaw,1990), is involved in replicon resetting in erythrocyte nuclei. Whileerythrocyte nuclei replicated efficiently when conditioned in theM-phase extract for 45 min prior to S-phase induction (FIG. 1 and FIG.5A), replication was slow when they were introduced into an M-phaseextract and then immediately driven into S phase (FIG. 5A). This showedthat it is not the M-S transition that is critical for reorganizing thenuclei for rapid replication, but rather the formation of mitoticmetaphase chromosomes. Consistent with this, erythrocyte nuclei thatwere incubated for 45 min in M-phase extract and then directlytransferred to an S-phase extract, but without Ca²⁺ activation, alsoreplicated as efficiently as sperm nuclei (Supplementary FIG. 3).

It has previously been observed that chicken erythrocyte nuclei do notcondense in topoisomerase II-depleted extracts (Adachi et al., 1991).Consistent with this, the Inventors found that the topoisomeraseII-specific inhibitor ICRF 193 (Oestergaard et al., 2004; Sato et al.,1997) prevented chromosome condensation in erythrocyte or sperm nucleiincubated in an M-phase extract (FIG. 5B). When erythrocyte nuclei wereincubated for 45 min in M-Phase extract containing ICRF 193, theInventors also obtained a very low rate of replication (FIG. 5A). TheInventors confirmed that the ICRF193-containing extract were still inmitosis by measuring H1 kinase activity (Supplementary FIG. 4). TheInventors also obtained similar results when erythrocytes were incubatedin topoisomerase II-depleted M-phase extracts (Supplementary FIG. 5). Incontrast, topoisomerase II inhibition or depletion did not affect thereplication of sperm chromatin in interphase egg extracts, as previouslypublished (Takasuga et al., 1995), although replication did deceleratein the final stages of DNA replication due to decatenation inhibition(Supplementary FIG. 5).

The Chromatin Source, not ORC Protein Levels, Influences InitiationFactor Recruitment

The Inventors next addressed the possibility that DNA topoisomerase IIdependant chromosomal organisation controls the efficiency of ORCrecruitment to chromatin. As shown in FIG. 5C, ORC2 did not bind toerythrocyte or sperm chromatin incubated in M-phase extracts, consistentwith previous reports (Romanowski et al., 1996). When S-phase entry wasinduced by Ca²⁺, ORC2 recruitment onto M-phase extract-treatederythrocyte chromatin was as efficient as it was onto sperm chromatin.ICRF 193 inhibition of topoisomerase II activity during mitoticremodeling, however, dramatically reduced the recruitment of ORC2 ontoerythrocyte, but not sperm chromatin for the subsequent S-phase (FIG.5C). This indicates that the topoisomerase II-dependent mitoticremodeling of erythrocyte nuclei is required for the proper recruitmentof ORC proteins in preparation for S phase.

It has been suggested that the absolute amount of replication factors inextracts can explain the observed high rates of DNA replication, andthat these factors are titrated by the DNA that accumulates during therapid divisions. This stoichiometric model was supported by theincreased replicon size observed when nuclei concentrations areincreased in Xenopus egg extracts (Walter and Newport, 1997). The data,however, showed that the concentration of replication proteins could notexplain the ability of M-phase extract to program nuclei for rapid DNAreplication. One limiting factor could be the ability of nuclei torecruit these proteins. Indeed, FIG. 5D shows that ORC2 is titrated byhigh concentrations of sperm nuclei, as previously reported (Rowles etal., 1996), but also that the chromatin context dominantly influencesthe efficiency of this recruitment. With sperm chromatin, the titrationcurve of ORC in the egg extract reached a plateau at 25 ng of DNA,equivalent to the amount in a midblastula-stage embryo (FIG. 5D, E). Asimilar titration curve was observed for MCM3, a subunit of the MCMhelicase complex involved in the initiation of DNA replication (data notshown). In contrast, erythrocyte chromatin did not bind ORC2 asefficiently as sperm chromatin (FIG. 5D, E), and the titration curve hadnot yet reached a plateau at 50 ng DNA. The recruitment of replicationinitiation factors is thus not only proportional to the amount ofavailable chromatin, but is also influenced by the chromatin's source.

Rearrangement of Chromatin Domains Occurs with Each Cell Cycle in EarlyXenopus Development.

In view of the above results, the Inventors investigated whether thesame chromatin reorganization occurs during early development in vivo.Early Xenopus cell cycles consist of overlapping S and M phases, with noG1 or G2. S phase is initiated at the metaphase-anaphase transition, asindividual chromosomes become surrounded by a nuclear membrane to formkaryomeres, and before nuclei are reconstructed by the fusion ofkaryomeres at telophase (FIG. 6A and (Lemaitre et al., 1998; Montag etal., 1988). The Inventors isolated the nuclear matrix either frompost-replicative, pre-mitotic nuclei (pre-MBT, 32-64 cell embryos), orfrom karyomeres subsequent to the metaphase-anaphase transition.Matrix-associated DNA was labeled and used to probe rDNA domain regions(as described above with erythrocyte nuclei; see FIG. 4A). As shown inFIG. 6B, while matrix-associated DNA from post-replicative nuclei wasrestricted to the rDNA intergenic spacer region, matrix-associated DNAfrom karyomeres was bound to all rDNA fragments, indicating randomassociation with the matrix. These data provide in vivo confirmationthat a major rearrangement of chromatin organization occurs at mitosis,and show that this reorganization occurs with each early embryonicdivision. The data further suggest that the rapid DNA replication seenduring early development involves the use of high numbers ofclosely-spaced, random attachment points between the chromatin and thenuclear matrix.

According to this interpretation, early mitoses might produce short DNAloop sizes to prepare chromatin for subsequent S phase. The loop sizewas measured both on karyomeres (S phase entry) or fully reconstitutedpost-replicative nuclei either from cycloheximide-synchronized earlyembryos at the 32-64 cell stage (Gard et al., 1990; Lemaitre et al.,1998) and Materials and Methods) or from unsynchronized embryos at the512-1024 cell stage (Supplementary FIG. 7). FIG. 6C shows thatkaryomeres had a mean loop size of 17.3+/−7.5 Kbp, similar to that oferythrocyte nuclei following passage through mitosis (FIG. 4F). Thisloop size also correlates with the replicon size previously measured invivo during Xenopus early development (Hyrien and Mechali, 1993). Theloop size increased to 59.7+/−10.7 Kbp in post-replicative earlyembryonic nuclei (FIG. 6C, and supplementary FIG. 7), confirming theexistence of a post-replicative remodeling process that increases thespacing between matrix attachment sites.

If mitotic resetting of chromatin to a short loop size were essentialfor high initiation rates, then post-replicative nuclei from earlyembryos that have not passed through mitosis would be incompetent forhigh rates of DNA replication. Indeed, although obtained from earlyembryos, post-replicative nuclei that were permeabilized and incubatedin an S-phase egg extract replicated slowly relative to sperm nuclei(FIG. 7A), and similarly to erythrocyte nuclei (FIG. 1B). FIG. 7B showsan alkaline agarose gel of nascent DNA that was labeled during DNAreplication. With sperm nuclei, strands grew to a value of around 9-10Kbp, followed by a shift to high molecular weight values, as expectedfrom the joining of replicated DNA from adjacent replicons. Withpost-replicative nuclei transferred to S phase, such a shift was notobserved. DNA replication was less efficient (FIG. 7A), as expected withmore widely-spaced replication origins, and a continuous stream ofstrands growing to larger sizes (>50 Kbp) was observed throughout thereaction. Finally, as previously observed with erythrocyte nuclei (FIG.5D, 5E), recruitment of ORC to chromatin was severely diminished,confirming that the efficiency of DNA replication during earlydevelopment is a matter of chromosome organization and not of theabsolute amount of ORC (Supplementary FIG. 8).

The Inventors next addressed whether the increase in loop size was apost-replicative event or occurred during DNA replication. As shown inFIGS. 7C and 7D, loop size increased gradually throughout S phase (FIG.7C, D), and this S-phase dependent increase could be prevented with ICRF(data not shown). Finally, the Inventors addressed whether entry intomitosis can reset the large loop size of post-replicative earlyembryonic nuclei, as previously shown for erythrocyte nuclei. FIG. 7Cshows that the loop size in post-replicative embryonic nuclei introducedinto M-phase egg extracts was dramatically reduced to 11.2+/−2.6 kbp, avalue equivalent to that of sperm chromatin following incubation inmitotic extract or at the beginning of S phase (FIG. 7). This mitoticremodeling of post-replicative nuclei was again blocked by thetopoisomerase II inhibitor ICRF193 (FIG. 7C). The Inventors concludethat entry into mitosis resets the loop size of both post-replicativeearly embryonic nuclei and differentiated nuclei to a low value.

Conclusion

The Dynamic Organization of Nuclear Structures for LWA ReplicationDuring Early Development

Xenopus early development provides a good illustration of the plasticityof the nuclear structure for adapting to rapid cell cycles (30 min) andDNA replication. Using cellular and biochemical techniques, theInventors describe here specific features of early nuclear organization,including non-specific anchorage of DNA to the nuclear matrix, shortloops, and a close mean spacing between replication origins.

The data, summarized in FIG. 8, indicate that at S phase entry in earlydevelopment, nuclei are organized into short loops and replicons,allowing recruitment of a large amount of ORC protein. At this stage,DNA replication initiates non-specifically (Hyrien et al., 1995). Loopsize increases progressively during S phase, and mitosis reprogramsnuclei so that they again include short loops and small replicons,enabling the rapid DNA replication of the early embryo. TopoisomeraseII, which has been previously identified as a major component of thechromosomal scaffold or matrix (Berrios et al., 1985; Earnshaw et al.,1985; Gasser et al., 1986), and which is required at an early stage ofchromosome condensation, is required for remodeling chromosomal loopsand thus for the reprogramming of nuclei for rapid replication.

A probable second, apparently-independent mechanism involves histoneacetylation, as inhibition of histone acetylases decreases replication,and this inhibition can be rescued by histone acetylase activators. Thesteady state endogeneous level of chromatin acetylation in earlyembryos, however, is sufficient for a maximum rate of sperm DNAreplication. The data cannot exclude the additional possibility that DNAreplication factors are regulated by acetylation (Takei et al., 2001).In either case, acetylation appears to be required for the acceleratedrate of DNA replication observed during early development.

DR Replication and Chromatin Domain Organization

ORC binding to chromatin has been shown to be linked to origin spacingin Xenopus egg extracts (Rowles et al., 1999; Walter and Newport, 1997).As ORC is absent from mitotic chromatin ((Romanowski et al., 1996) andFIG. 5C), the results indicate that mitotic remodeling occursindependently of pre-RC establishment. At the same time, mitoticremodeling, and the associated decrease in loop size, enhances theability of chromatin to bind ORC. While chromatin-bound ORC increaseswith the amount of sperm chromatin, at least until the MBT (4,000 to8,000 cells), the increase is several times lower in post-replicativeembryonic nuclei and erythrocyte nuclei. In these nuclei, decreased ORCbinding occurs in striking conjunction with an increased DNA loop size,and inhibiting loop size remodeling with ICRF-93 decreases ORCrecruitment. A maximum number of ORC-binding sites, corresponding tomultiple matrix anchorage sites, might explain the high density ofreplication initiation sites prior to the MBT. While no strict DNAsequence specificity has been detected for ORC proteins in metazoans orin fission yeast, yeast ORC4 specifically binds to asymmetric AT richsequences (Chuang and Kelly, 1999), and Xenopus ORC preferentiallyassociates with AT rich regions (Kong et al., 2003). AT rich regions areenriched at matrix associated regions (MAR), and this may provide abasal nuclear architecture for DNA replication.

Chromosomal Architecture at Mitosis, Replicon Resetting, and Cloning

A major issue in nuclear transfer experiments is how genetic orepigenetic marks within differentiated nuclei can be erased, as failureto do so decreases cloning efficiency. Cloning success is increased byserial transfer, in which donor nuclei are obtained from embryos thathave passed through successive cell divisions following an initialtransfer (Gurdon, 1962). The data explain this observation, and suggestthat formation of chromosomes at mitosis is an important element in thegenetic reprogramming that occurs in successful nuclear transplantation,permitting the restructuring of adult nuclei for rapid embryonic DNAreplication.

One model that has been proposed to explain why Xenopus nucleartransplants often fail to develop invokes a cytoplasmic clock thatimposes cell division every 30 minutes during early development (Hara etal., 1980). In terms of this model, nuclei from differentiated cellsthat have not been reprogrammed by the time mitosis begins will not becompletely replicated, leading to abortive cleavage. Prior exposure to amitotic egg extract, however, may allow them to keep up with the cellcycle clock by allowing an increased number of replication origins.

The data suggest that it is metaphase, and not the metaphase-anaphasetransition, that resets the replicon organization. In classical nucleartransfer, when a somatic donor nuclei is introduced into an egg, the eggis simultaneously activated, triggering an immediate exit from metaphaseof the second division and thereby preventing mitotic chromosomes fromforming. Significantly, when erythrocyte nuclei are introduced into Mphase extracts and immediately driven into S phase, they fail toreplicate efficiently. The Inventors found that such nuclei can only beremodeled and efficiently participate in subsequent DNA replication whenthey are placed in a mitotic environment for 45 min prior to activation(FIG. 1B). Several lines of evidence indicate that the crucial parametercontrolling this phenomenon is the organization of metaphase mitoticchromosomes, not the concentration of replication factors. First, theInventors found that the stoichiometry between replication initiationfactors and available chromatin cannot explain the observed rates of ORCrecruitment and DNA replication. Second, M phase induces a global changein the chromosomal architecture, leading to a dramatic shortening ofchromosome loop size. Third, topoisomerase II, which is involved inregulating chromosomal architecture and has been identified at the baseof the loop domains (Adachi et al., 1989; Earnshaw et al., 1985; Gasseret al., 1986; Iarovaia et al., 1995), is necessary for ORC recruitmentas well as the shortening of both loop size and inter-origin spacing.

The data may also explain observations showing that the specification ofDNA replication origins occurs between the middle and end of G1 phase(Wu and Gilbert, 1996). During early Xenopus development, S phase and Mphase occur successively without G1. Following the chromatinreprogramming that occurs in mitosis, this lack of G1 may preventspecific origins from being established, resulting in S-phase withoutspecified origins. This required mitotic reprogramming of the repliconand chromosome structure can also explain the observed benefit of theuse of half-cleaved embryos as a donor source in animal cloning byserial transfer (Gurdon and Laskey, 1970; Gurdon et al., 1975).Specifically, as such nuclei were presumably exposed to a mitoticcontext in a first unsuccessful cleavage, they may have beenreprogrammed through the mechanism described here. The mechanism alsoprovides an explanation for recent improvements in human cloning methodsin which a two-hour incubation between nuclear injection and eggactivation increases the cloning efficiency (Hwang et al., 2005).

Because the sperm and egg nuclei replicate before karyogamy, theInventors expect that they must be organized for rapid DNA replicationby the time they fuse, before the first mitotic division. Indeed, beforefertilization occurs the egg nucleus is blocked at metaphase and istherefore already organized into mitotic chromosomes. In addition, theInventors observed that sperm nuclei were organized into short loopsbefore fertilization, indicating that both the male and female pronucleiare already set for rapid replication at fertilization. Theseobservations underscore the fact that it is unfertilized eggs, but notactivated or fertilized eggs, that are capable of conditioningdifferentiated nuclei for development.

Example 2 Method for Increasing Cloning Efficiency Material and Methods

Xenopus egg mitotic extracts are used to form mitotic chromosomes from anucleus of a differentiated somatic cell, in order to improve theefficiency of the cloning by nuclear transfer.

The nuclei are purified as follows: the cells are collected andcentrifuged at 1000 g for 10 minutes. The cells are washed with PBSbefore being centrifuged at 1000 g for 10 minutes. Then, the cells areresuspended in 10 ml of a cold hypotonic buffer (4° C.) (HB: 10 mMK/Hepes pH 7.7, 10 mM KCl, 1 mM NaCl, 2 mM MgCl₂, 1 mM EGTA), beforebeing transferred in a dounce homogenizer tight pestle B for 10 minutes,until the cells are swelled. Then, the dounce strokes are carried outuntil the cellular membrane has disappeared (10 to 15 dounce strokes,depending on the cell type). The mixture is then centrifuged at 1000 gfor 10 minutes. The pellet is resuspended in a hypotonic buffer 0.1%Triton X100. The nuclei are purified through a sucrose cushion ofsucrose 0.7 M and resuspended in a remodeling buffer RB (10 mM Hepes/KpH 7.3, 100 mM KCl, 0.1 mM CaCl₂, 1 mM MgCl₂, 50 mM sucrose).

The mitotic remodeling is carried out by mixing 22 μl of Xenopus eggmitotic extract with 2.5 μl of E mix (200 μg/ml creatine kinase, 200 mMcreatine phosphate, 20 mM ATP, 20 mM MgCl₂, 2 mM EGTA) and 0.5 μl ofdifferentiated and purified nuclei (500 nuclei/μl of extract). Themixture is incubated for 45 minutes (up to 1 hour 30 minutes) at 23° C.in order to form chromosomes.

When cloning is performed from cells, and not from the purified nuclei,the cells are first possibly permeabilized as follows: cultured cellsare washed with PBS and are resuspended in a permeabilization buffer(CPB: 10 mM K/Hepes pH 7.7, 100 mM KCl, 5 mM NaCl, 2 mM MgCl₂, 1 mM EGTAprotease inhibitors, Leupeptin, Pepstatin, Aprotinin at 10 μg/ml) cooleddown on ice adjusted at 10.10⁶/ml. Digitonin at a final concentration of30 μg/ml. is added for 5 min at 4° C. The reaction is then stopped byadding 10 volumes of PB, protease inhibitors. The mixture is centrifugedat 1000 g for 10 minutes, and the cells are resuspended at 10⁸ cells/mlof PB, 10% glycerol, protease inhibitors. Freshly prepared cells areused. The mitotic remodeling is then carried out as previously, at aconcentration of around 500 cells/μl of extract.

Cells or nuclei are then injected in an enucleated ovule to trigger thedevelopment. This protocol may be used for cells of different animalspecies.

Results

Animal cloning is now possible but used with low yields of success thatdiffer between species. The Inventors have demonstrated the ability of aXenopus egg extract to reprogram a nucleus of a differentiated somaticcell. During early embryogenesis of Xenopus, the S-phase length isreduced to 15 minutes, whereas the S-phase generally lasts 6-8 hours ina somatic cell. This replication rate is particularly high because of anincrease in the number of replication origins which function on thegenome upon each cycle in an almost synchronous way.

The results of the Inventors show that the reprogramming of adifferentiated nucleus can only occur during the incubation with amitotic extract, which leads to the formation of metaphase chromosomes.The Inventors have then measured the ability of the reprogrammed nucleusto reproduce a replication phase which is characteristic of the earlydevelopment, with a number of replication origins corresponding to anembryo of this stage. This reprogramming occurs through a completegenome reorganization to adapt the genome to short cycles (Lemaitre etal., 2005, 123(5):787-801)). The Inventors have also demonstrated thatthis phenomenon of genome adaptation is a main phenomenon of the embryowhich operates upon each cycle, which ensures a complete duplication ofthe genome before mitosis, otherwise leading to a genomic instability.

Example 3 Method for Obtaining Stem Cells from a Differentiated SomaticCell

The following process may be used for obtaining stem cells from any kindof differentiated somatic cell.

The cells, for example blood cells, are purified and permeabilized asfollows: the cultured cells are washed in 10 ml PBS, then centrifuged at1000 g for 10 min. The cell pellet is resuspended in 10 ml ofpermeabilization buffer PB (10 mM K/Hepes pH 7.7, 100 mM KCl, 5 mM NaCl,2 mM MgCl₂, 1 mM EGTA). The cells are centrifuged at 1000 g for 10 minand the cell pellet is resuspended in PB, protease inhibitors (mix ofLeupeptin, Pepstatin, Aprotinin, each at 10 μg/ml). The cells are thenput on ice and adjusted to a concentration of 10.10⁶ cells/ml.

The cells are permeabilized by adding digitonin (30 mg/ml of a stocksolution) at a final concentration of 30 μg/ml, for 5 min on ice (4°C.). The reaction is stopped by adding 10 volumes of PB, proteaseinhibitors. The cells are then centrifuged at 1000 g for 10 min.

In a typical remodeling reaction, 22 μl of M phase extract are mixedwith 0.5 μl of permeabilized cells or nuclei (500 nuclei or cells/μlextract). The mixture is incubated at 23° C. for 45 min. The cells arethen washed in PBS to remove the cell extract and are seeded in aculture plate.

REFERENCES

-   Adachi, Y., Kas, E., and Laemmli, U. K. (1989). Preferential,    cooperative binding of DNA topoisomerase II to scaffold-associated    regions. Embo J 8, 3997-4006.-   Adachi, Y., and Laemmli, U. K. (1992). Identification of nuclear    pre-replication centers poised for DNA synthesis in Xenopus egg    extracts: immunolocalization study of replication protein A. J Cell    Biol 119, 1-15.-   Adachi, Y., Luke, M., and Laemmli, U. K. (1991). Chromosome assembly    in vitro: topoisomerase II is required for condensation. Cell 64,    137-148.-   Aggarwal, B. D., and Calvi, B. R. (2004). Chromatin regulates origin    activity in Drosophila follicle cells. Nature 430, 372-376.-   Almouzni, G., and Mechali, M. (1988). Assembly of spaced chromatin    promoted by DNA synthesis in extracts from Xenopus eggs. Embo J 7,    665-672.-   Balasubramanyam, K., Swaminathan, V., Ranganathan, A., and    Kundu, T. K. (2003). Small molecule modulators of histone    acetyltransferase p300. J Biol Chem 278, 19134-19140.-   Berezney, R., Dubey, D. D., and Huberman, J. A. (2000).    Heterogeneity of eukaryotic replicons, replicon clusters, and    replication foci. Chromosoma 108, 471-484.-   Berezney, R., Mortillaro, M. J., Ma, H., Wei, X., and    Samarabandu, J. (1995). The nuclear matrix: a structural milieu for    genomic function. Int Rev Cytol, 1-65.-   Berrios, M., Osheroff, N., and Fisher, P. A. (1985). In situ    localization of DNA topoisomerase II, a major polypeptide component    of the Drosophila nuclear matrix fraction. Proc Natl Acad Sci USA    82, 4142-4146.-   Blow, J. J., and Laskey, R. A. (1986). Initiation of DNA replication    in nuclei and purified DNA by a cell-free extract of Xenopus eggs.    Cell 47, 577-587.-   Buongiorno-Nardelli, M., Micheli, G., Carri, M. T., and Marilley, M.    (1982). A relationship between replicon size and supercoiled loop    domains in the eukaryotic genome. Nature 298, 100-102.-   Chuang, R. Y., and Kelly, T. J. (1999). The fission yeast homologue    of Orc4p binds to replication origin DNA via multiple AT-hooks. Proc    Natl Acad Sci USA 96, 2656-2661.-   Cook, P. R., and Brazell, I. A. (1975). Supercoils in human DNA. J    Cell Sci 19, 261-286.-   Cook, P. R., and Brazell, I. A. (1976). Conformational constraints    in nuclear DNA. J Cell Sci 22.-   Coue, M., Kearsey, S. E., and Mechali, M. (1996). Chromotin binding,    nuclear localization and phosphorylation of Xenopus cdc21 are    cell-cycle dependent and associated with the control of initiation    of DNA replication. Embo J 15, 1085-1097.-   Danis, E., Brodolin, K., Menut, S., Maiorano, D., Girard-Reydet, C.,    and Mechali, M. (2004). Specification of a DNA replication origin by    a transcription complex. Nat Cell Biol 6, 721-730.-   DiBerardino, M. A., and Hoffner, N. J. (1983). Gene reactivation in    erythrocytes: nuclear transplantation in oocytes and eggs of Rana.    Science 219, 862-864.-   Dijkwel, P. A., Vaughn, J. P., and Hamlin, J. L. (1991). Mapping of    replication initiation sites in mammalian genomes by two-dimensional    gel analysis: stabilization and enrichment of replication    intermediates by isolation on the nuclear matrix. Mol Cell Biol 11,    3850-3859.-   Earnshaw, W. C., Halligan, B., Cooke, C. A., Heck, M. M., and    Liu, L. F. (1985). Topoisomerase II is a structural component of    mitotic chromosome scaffolds. J Cell Biol 100, 1706-1715.-   Firmbach-Kraft, I., and Stick, R. (1995). Analysis of nuclear lamin    isoprenylation in Xenopus oocytes: isoprenylation of lamin B3    precedes its uptake into the nucleus. J Cell Biol 129, 17-24.-   Francon, P., Lemaitre, J. M., Dreyer, C., Maiorano, D., Cuvier, O.,    and Mechali, M. (2004). A hypophosphorylated form of RPA34 is a    specific component of pre-replication centers. J Cell Sci 117,    4909-4920.-   Gard, D. L., Hafezi, S., Zhang, T., and Doxsey, S. J. (1990).    Centrosome duplication continues in cycloheximide-treated Xenopus    blastulae in the absence of a detectable cell cycle. J Cell Biol    110, 2033-2042.-   Gasser, S. M., and Laemmli, U. K. (1986). Cohabitation of scaffold    binding regions with upstream/enhancer elements of three    developmentally regulated genes of D. melanogaster. Cell 46,    521-530.-   Gasser, S. M., Laroche, T., Falquet, J., Boy de la Tour, E., and    Laemmli, U. K. (1986). Metaphase chromosome structure. Involvement    of topoisomerase II. J Mol Biol 188, 613-629.-   Gurdon, J. B. (1962). The developmental capacity of nuclei taken    from intestinal epithelium cells of feeding tadpoles. J Embryol Exp    Morphol 10, 622-640.-   Gurdon, J. B., Byrne, J. A., and Simonsson, S. (2003). Nuclear    reprogramming and stem cell creation. Proc Natl Acad Sci USA 100    Suppl 1, 11819-11822.-   Gurdon, J. B., and Laskey, R. A. (1970). The transplantation of    nuclei from single cultured cells into enucleate frogs' eggs. J    Embryol Exp Morphol 24, 227-248.-   Gurdon, J. B., Laskey, R. A., and Reeves, O. R. (1975). The    developmental capacity of nuclei transplanted from keratinized skin    cells of adult frogs. J Embryol Exp Morphol 34, 93-112.-   Hara, K., Tydeman, P., and Kirschner, M. (1980). A cytoplasmic clock    with the same period as the division cycle in Xenopus eggs. Proc    Natl Acad Sci USA 77, 462-466.-   Hozak, P., Hassan, A. B., Jakson, D. A., and Cook, P. R. (1993).    Visualization of replication factories attached to a nucleoskeleton.    Cell 73, 361-373.-   Hwang, W. S., Roh, S. I., Lee, B. C., Kang, S. K., Kwon, D. K., Kim,    S., Kim, S. J., Park, S. W., Kwon, H. S., Lee, C. K., et al. (2005).    Patient-specific embryonic stem cells derived from human SCNT    blastocysts. Science 308, 1777-1783.-   Hyrien, O., Maric, C., and Mechali, M. (1995). Transition in    specification of embryonic metazoan DNA replication origins. Science    270, 994-997.-   Hyrien, O., and Mechali, M. (1993). Chromosomal replication    initiates and terminates at random sequences but at regular    intervals in the ribosomal DNA of Xenopus early embryos. Embo J 12,    4511-4520.-   Iarovaia, O. V., Lagarkova, M. A., and Razin, S. V. (1995). The    specificity of human lymphocyte nucleolar DNA long-range    fragmentation by endogenous topoisomerase II and exogenous Bal 31    nuclease depends on cell proliferation status. Biochemistry 34,    4133-4138.-   Ioudinkova, E., Petrov, A., Razin, S. V., and Vassetzky, Y. S.    (2005). Mapping long-range chromatin organization within the chicken    alpha-globin gene domain using oligonucleotide DNA arrays. Genomics    85, 143-151.-   Jackson, D. A. (1990). The organization of replication centres in    higher eukaryotes. Bioessays 12, 87-89.-   Kong, D., Coleman, T. R., and DePamphilis, M. L. (2003). Xenopus    origin recognition complex (ORC) initiates DNA replication    preferentially at sequences targeted by Schizosaccharomyces pombe    ORC. Embo J 22, 3441-3450.-   Lemaitre, J. M., Bocquet, S., Buckle, R., and Mechali, M. (1995).    Selective and rapid nuclear translocation of a c-Myc-containing    complex after fertilization of Xenopus laevis eggs. Mol Cell Biol    15, 5054-5062.-   Lemaitre, J. M., Bocquet, S., and Mechali, M. (2002). Competence to    replicate in the unfertilized egg is conferred by Cdc6 during    meiotic maturation. Nature 419, 718-722.-   Lemaitre, J. M., Geraud, G., and Mechali, M. (1998). Dynamics of the    genome during early Xenopus laevis development: karyomeres as    independent units of replication. J Cell Biol 142, 1159-1166.-   Leno, G. H., and Laskey, R. A. (1991). The nuclear membrane    determines the timing of DNA replication in Xenopus egg extracts. J    Cell Biol 112, 557-566.-   Leonard, R. A., Hoffner, N. J., and DiBerardino, M. A. (1982).    Induction of DNA synthesis in amphibian erythroid nuclei in Rana    eggs following conditioning in meiotic oocytes. Dev Biol 92,    343-355.-   Lohka, M. J., and Masui, Y. (1983). Formation in vitro of sperm    pronuclei and mitotic chromosomes induced by amphibian ooplasmic    components. Science 220, 719-721.-   Lu, Z. H., Xu, H., and Leno, G. H. (1999). DNA replication in    quiescent cell nuclei: regulation by the nuclear envelope and    chromatin structure. Mol Biol Cell 10, 4091-4106.-   McKay, R. (2000). Stem cells—hype and hope. Nature 406, 361-364.-   Menut, S., Lemaitre, J. M., Hair, A., and Méchali, M. (1999). DNA    replication and chromatin assembly using Xenopus egg extracts,    Oxford University Press, Ed J. D. Richter).-   Michalet, X., Ekong, R., Fougerousse, F., Rousseaux, S., Schurra,    C., Hornigold, N., van Slegtenhorst, M., Wolfe, J., Povey, S.,    Beckmann, J. S., and Bensimon, A. (1997). Dynamic molecular combing:    stretching the whole human genome for high-resolution studies.    Science 277, 1518-1523.-   Montag, M., Spring, H., and Trendelenburg, M. F. (1988). Structural    analysis of the mitotic cycle in pre-gastrula Xenopus embryos.    Chromosoma 96, 187-196.-   Murray, A. W. (1991). Cell cycle extracts. Methods Cell Biol 36,    581-605.-   Nakayasu, H., and Berezney, R. (1989). Mapping replicational sites    in the eucaryotic cell nucleus. J Cell Biol 108, 1-11.-   Neri, L. M., Mazzotti, G., Capitani, S., Maraldi, N. M., Cinti, C.,    Baldini, N., Rana, R., and Martelli, A. M. (1992).-   Nuclear matrix-bound replicational sites detected in situ by    5-bromodeoxyuridine. Histochemistry 98, 19-32.-   Oestergaard, V. H., Knudsen, B. R., and Andersen, A. H. (2004).    Dissecting the cell-killing mechanism of the topoisomerase    II-targeting drug ICRF-193. J Biol Chem 279, 28100-28105.-   Pardoll, D. M., and Vogelstein, B. (1980). Sequence analysis of    nuclear matrix associated DNA from rat liver. Exp Cell Res 128,    466-470.-   Pasero, P., Bensimon, A., and Schwob, E. (2002). Single-molecule    analysis reveals clustering and epigenetic regulation of replication    origins at the yeast rDNA locus. Genes Dev 16, 2479-2484.-   Paulson, J. R., and Laemmli, U. K. (1977). The structure of    histone-depleted metaphase chromosomes. Cell 12, 817-828.-   Romanowski, P., Madine, M. A., Rowles, A., Blow, J. J., and    Laskey, R. A. (1996). The Xenopus origin recognition complex is    essential for DNA replication and MCM binding to chromatin. Curr    Biol 6, 1416-1425.-   Rowles, A., Chong, J. P., Brown, L., Howell, M., Evan, G. I., and    Blow, J. J. (1996). Interaction between the origin recognition    complex and the replication licensing system in Xenopus. Cell 87,    287-296.-   Rowles, A., Tada, S., and Blow, J. J. (1999). Changes in association    of the Xenopus origin recognition complex with chromatin on    licensing of replication origins. J Cell Sci 112, 2011-2018.-   Ryan, J., Llinas, A. J., White, D. A., Turner, B. M., and    Sommerville, J. (1999). Maternal histone deacetylase is accumulated    in the nuclei of Xenopus oocytes as protein complexes with potential    enzyme activity. J Cell Sci 112 (Pt 14), 2441-2452.-   Sato, M., Ishida, R., Ohsumi, K., Narita, T., and Andoh, T. (1997).    DNA topoisomerase II as the cellular target of a novel antitumor    agent ICRF-193, a bisdioxopiperazine derivative, in Xenopus egg    extract. Biochem Biophys Res Commun 235, 571-575.-   Takasuga, Y., Andoh, T., Yamashita, J., and Yagura, T. (1995).    ICRF-193, an inhibitor of topoisomerase II, demonstrates that DNA    replication in sperm nuclei reconstituted in Xenopus egg extracts    does not require chromatin decondensation. Exp Cell Res 217,    378-384.-   Takei, Y., Swietlik, M., Tanoue, A., Tsujimoto, G., Kouzarides, T.,    and Laskey, R. (2001). MCM3AP, a novel acetyltransferase that    acetylates replication protein MCM3. EMBO Rep 2, 119-123.-   Tunquist, B. J., and Maller, J. L. (2003). Under arrest: cytostatic    factor (CSF)-mediated metaphase arrest in vertebrate eggs. Genes Dev    17, 683-710.-   Vassetzky, Y., Hair, A., and Mechali, M. (2000). Rearrangement of    chromatin domains during development in Xenopus. Genes Dev 14,    1541-1552.-   Versini, G., Comet, I., Wu, M., Hoopes, L., Schwob, E., and    Pasero, P. (2003). The yeast Sgs1 helicase is differentially    required for genomic and ribosomal DNA replication. Embo J 22,    1939-1949.-   Vogelstein, B., Pardoll, D. M., and Coffey, D. S. (1980).    Supercoiled loops and eucaryotic DNA replication. Cell 22, 79-85.-   Wade, P. A., Jones, P. L., Vermaak, D., and Wolffe, A. P. (1999).    Purification of a histone deacetylase complex from Xenopus laevis:    preparation of substrates and assay procedures. Methods Enzymol 304,    715-725.-   Walter, J., and Newport, J. (2000). Initiation of eukaryotic DNA    replication: origin unwinding and sequential chromatin association    of Cdc45, RPA, and DNA polymerase alpha. Mol Cell 5, 617-627.-   Walter, J., and Newport, J. W. (1997). Regulation of replicon size    in Xenopus egg extracts. Science 275, 993-995.-   Wood, E. R., and Earnshaw, W. C. (1990). Mitotic chromatin    condensation in vitro using somatic cell extracts and nuclei with    variable levels of endogenous topoisomerase II. J Cell Biol 111,    2839-2850.-   Wu, J. R., and Gilbert, D. M. (1996). A distinct G1 step required to    specify the Chinese hamster DHFR replication origin. Science 271,    1270-1272.-   Wu, J. R., Yu, G., and Gilbert, D. M. (1997). Origin-specific    initiation of mammalian nuclear DNA replication in a Xenopus    cell-free system. Methods 13, 313-324.

The invention claimed is:
 1. A composition comprising: an extract offirst cells to which an amount of EGTA sufficient to chelate Ca2+activity has been added, said first cells being female germinal cells(egg) in M-phase of the cell cycle; and at least a second cell, saidsecond cell containing a nucleus, wherein both said first and secondcells originate from a pluricellular organism, wherein the second cellis a cell originating from a multicellular organism selected from thegroup consisting of Xenopus, mouse and human, and wherein said extractof first cells is a Xenopus eggs extract.
 2. The composition accordingto claim 1, wherein said second cell is a differentiated somatic cell.3. The composition according to claim 1, wherein said at least a secondcell is permeabilized.
 4. The composition according to claim 1, whereinsaid extract of first cells contain EGTA in an amount from 0.1 mM to 5mM of said extract.
 5. The composition according to claim 1, whereinsaid extract of first cells contain EGTA in an amount 1 mM or 2 mM ofsaid extract.
 6. The composition according to claim 2, wherein saiddifferentiated somatic cell is selected from the group consisting ofskin, intestine, liver, blood and muscle cell.
 7. The compositionaccording to claim 1, comprising an extract of first cells which arefemale germinal cells (egg) in M-phase of the cell cycle; from 0.1 mM to5 mM EGTA; and at least a second cell, said second cell containing anucleus.
 8. The composition according to claim 1, in association with apharmaceutically acceptable carrier.